18-57588259-C-T

Variant names:

• chr18-57588259-C-T
• rs34779648

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.156 in 152,240 control chromosomes in the GnomAD database, including 2,142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2142 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23756 AN: 152122 Hom.: 2142 Cov.: 33

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.151

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23760 AN: 152240 Hom.: 2142 Cov.: 33 AF XY: 0.157 AC XY: 11663 AN XY: 74422

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.148

Alfa AF: 0.163 Hom.: 276

Bravo AF: 0.147

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	1.0
DANN	Benign	0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34779648; hg19: chr18-55255491;